Posted
by
ScuttleMonkey
on Saturday April 08, 2006 @01:14PM
from the good-for-some-bad-for-others dept.

pnewhook writes "The New York Times is reporting that 'by reconstructing ancient genes from long-extinct animals, scientists have for the first time demonstrated the step-by-step progression of how evolution created a new piece of molecular machinery by reusing and modifying existing parts. The researchers say the findings, published today in the journal Science, offer a counterargument to doubters of evolution who question how a progression of small changes could produce the intricate mechanisms found in living cells.'"

It was only a matter of time before scientists discovered the steps and had enough knowledge to connect the dots.

Frankly, I'm glad they're finding more and more of how biology works. I don't want to get into a creationist debate, but it has always astounded me that people would argue that life is too complex for it to have been made "naturally" and that a higher being must have helped along the way. But, by saying that, they're saying that God is not powerful enough to create such a universe in which evolution can happen, that a universe created by God could not possibly work by itself.

But it does kinda reduce the likelihood that there is a PERSONAL god who is intimately concerned with all of our activities, and so is a reason to behave in a moral way and more importantly, to then worship that god and tithe to the church who claims to be the bridge between man and god.

(Note, I was not saying that atheists are not moral with the "is a reason to behave..." line, but for some people the existance of a personal god is one of the reasons to behave in a moral manner.)

Not at all. I'm an atheist, but I welcome imaginative, honest theist thinkers like biologist Kenneth Miller who feel that, if anything, evolution BETTER fits this theology than the reverse. A universe in which God allows to develop on its own, and then reaches out PERSONALLY to sentient creatures (and even performs miracles as part of this reaching out) is far more "free" than one in which God is constantly micro-managing.

Now, I don't believe in God, but I bear no grudges against those who do, and as long as a belief doesn't involve scientific claims or attacking good science with falsehoods, but I applaud those who are taking their beliefs forward and refining them to make them more honest rather than simply defending dogma. If there were a God, the only kind I can possibly imagine would reward the former, not the latter.

But it does kinda reduce the likelihood that there is a PERSONAL god who is intimately concerned with all of our activities, and so is a reason to behave in a moral way and more importantly, to then worship that god and tithe to the church who claims to be the bridge between man and god.

Personally, I feel like events such as hurricane Katrina, the tsunami in the indian ocean, and September 11th offer a much stronger proof of the lack of a personal god.

Interestingly, other people look at the same events and come to the exact opposite conclusion.

Personally, I feel like events such as hurricane Katrina, the tsunami in the indian ocean, and September 11th offer a much stronger proof of the lack of a personal god.

Either that, or at least strong proof that if there IS a god, he/she's a sadistic bastard without anything resembling our idea of morality, justice, or fairness. In other words, any god that regularly lets shit like this happen deserves our scorn, not our adoration.

But it does kinda reduce the likelihood that there is a PERSONAL god who is intimately concerned with all of our activities

Why?

What if the myriad quantum fluctuations that we observe as "random" are, every single one of them, directed by just such a god? What could be more "intimately concerned with all of our activities" than directing every single subatomic event?

"Random" is a description, not an explanation. What if the statistical probabilities that we observe that say that particle X will de

However, the likelihood that God is intimately concerned with our lives is a question completely independent of science, and cannot be considered to have been demonstrated to be more or less likely, no matter what science discovers.

Well, if there's a personal God intimately concerned with our lives, then the fact that he caused or at least did not prevent the tsunami shows that his priorities are extremely strange indeed. He then certainly cannot be described as "good" in any of the word's standard sense

My point remains. You, and the GGP are both arguing that, because we don't know God's masterplan, that natural disasters could be a good thing. That's an argument to ignorance, and you're using it to justify the sufferng caused by those natural disasters.

And, yes, people have the choice to not buy into such fallacious arguments; most rational people don't since anyone with a basic understanding of logical fallacies can see the inherent flaw in such reasoning, not to mention the obvious insensitivity it sho

I never said this DISPROVES a personal god, but it does show that the personal god as described in... well... most western monotheistic religions is not actually necessary for us to have gotten from a single cell floating around in a broth to the walking, thinking, complex organism that we are today. This makes the existance of that god less likely, as there is an alternative path of events that could have happened, as defined by natural laws, for us to get where we are today.

Sorry to nitpick, but quantum "fluctuations" are not random. People often confuse the terms "random" and "probabilistic" when they talk about quantum physics. A "random" system is a system where any outcome of measurement is just as likely as any other outcome. However, quantum particles are more likely to be at the expectation value of position than at any other place, though there is a NON-zero probability of it being anywhere else in the system. So quantum "fluctuations"(I'm not sure what you mean by this) are NOT random, because some outcomes of measurement are vastly more likely than others. The only requirement for a quantum particle is that the probability of it being SOMEWHERE is 1.

Quantum particles are associated with probability WAVES that fluctuate with time. When we say wave-particle duality we mean that the particle does NOT have a definite classical trajectory but instead a WAVE of probability associated with it that describes the positions, energies, and momentums at which the particle is most likely to be. This is called a wave function; it is a solution to Schrodinger's differential wave equation and its square is a probability curve.

Depending on your interpretation, quantum mechanics does indicate some things about reality such as there is an ONTOLOGICAL limit on what we can know for certain about objective reality such that it appears meaningless to talk about an absolute objective reality at all. That is, reality changes by being observed. However, unlike general relativity which does indeed EXPLAIN gravity by saying that gravity is identical with a curved space-time geometry, you are quite right in saying that quantum mechanics does not explain anything. Nor does particle theory or E&M explain why there are electric and magnetic forces without beginning to conjure up force-carrying particles and the like. They are currently trying to explain all these things by means of string theory.

It's designed to "naturally" evolve to what we are. God is powerful enough to create a universe in which evolution can happen...as designed. I don't have a problem with that.We'll need to figure most ALL the steps (especially the difficult, rare ones), and the probability that everything happened by change...and then believing things just happen (God by change) or believing that there's some highly improbable that happened (God, not chance) will still depend on a matter of chance. We'll never be able to con

Another is to point out evolution's flaws (something evolutionists get very testy about, btw. They don't like their faith questioned anymore than religious people do)

This is simply not true. Evolutionary biologists find flaws in existing theories of evolution fairly often, and the theories are adjusted accordingly over time. This is simply how all science, including biology, works; there is no crisis of faith as you claim.

"Another is to point out evolution's flaws (something evolutionists get very testy about, btw. They don't like their faith questioned anymore than religious people do)"

It's easy to make this accusation, but intellectually lazy.

I'd say that scientists spend more time picking apart each others flaws and mistakes than in almost any other realm of life. What they get testy about is people who haven't bothered to actually study the debates, who know next to nothing about the subjects they are talking about, spreading falsehoods or gross misrepresentations of science. Worse, even when these ideas are debunked or even admitted as wrong by the people making them, they then still get brought up over and over again to new audiences. How many times have you heard the "evolution can't add new information" or "if we evolved from apes, how come there are still apes" nonsense? If people seemed determined to spread lies and falsehoods about me personally, I'd certainly get "testy." But not because anyone was questioning my "faith."

"The parent poster cannot proclaim the virtues of modern knowledge, lump all people of faith into one statement, then chastise them. THAT, my friend, is intellectually lazy."

Agreed. But then, most people use the term "creationist" to refer to YECs or other denialists. There are many theistic evolutionists who could be called creationists too, but whom have no conflict with mainstream science. But I'm not sure even they would identify with a criticism aimed at creationists.

What you claim about people trolling is true, but trivial. Sure, for ANY point of view you can point to a couple of knuckleheads. But that's a pretty weak way to attack science in general, and claim that evolution is a "faith" that people are mad about anyone criticizing. Of course, if you can show me a criticism that's actually accurate and informed, I'll be very surprised. There are a number of very real hotly debated controversies within mainstream biology. But I've never, not once, seen any creationist mention them.

No, you are simply wrong about the need for faith as far as evolution goes. Because science doesn't deal in truth, it doesn't require faith. Science deals in likelihoods. Given X what is the chance of Y assuming Z. As a professional scientist I don't believe that the scientific method unviels truth. I don't have to. It isn't my job to get truth. I get scientific facts, and model them with scientific theories. They don't have to be true because I don't care about them being true. I care about the uncertainty

The flipside of the evolutionary topic is, well, what if we just say there is no God and move on?I do not see how this is, in any way, an "evolutionary topic". The theory of evolution says nothing whatsoever regarding the subject of deities.

Dismissing the existence of God in no way advances the human condition.

To which "God", out of the thousans of deities worshipped and acknowledged throughout human history, do you refer and why do you reference that particular deity to the exclusion of all others?

Dr. Behe described the results as "piddling." He wondered whether the receptors with the intermediate mutations would be harmful to the survival of the organisms and said a two-component hormone-receptor pair was too simple to be considered irreducibly complex. He said such a system would require at least three pieces and perform some specific function to fit his notion of irreducibly complex.

What Dr. Thornton has shown, Dr. Behe said, falls within with incremental changes that he allows evolutionary processes can cause.

"Even if this works, and they haven't shown that it does," Dr. Behe said, "I wouldn't have a problem with that. It doesn't really show that much."

He will never give up as long as he can keep moving the goalposts.

It's truly an intellectually dishonest practice and it speaks directly to the kind of Doctor Behe is. This is the guy who testified in that 'lets put ID into the classroom' trial in Dover, PA. His testimony was an embarrassement and I'm surprised he has enough credibility left that the NY Times would include him in their article. I guess it's the whole "two sides of an argument" theme again.

True, though the article states that other ID proponents have cited it as an example.Behe's statement provokes an interestingly falsifiable challenge. Using the techniques developed for this study, it may be possible to find a system of at least three pieces performing some purpose, as he suggests. He's still got wiggle room in there should somebody discover that (especially in the word "purpose"), but he'll find himself increasingly marginalized if somebody manages to meet his challenge. (Not that he's no

But those several orders of magnitude are just a constant factor. What the research has done is really like proving a problem is solvable in Polynomial time when a bunch of people have been arguing that it's NP.

The televangelists didn't need to "figure out" anything. Religion's already been a business for millennia. The televangelists are simply continuing a tradition that's been going on ever since ancient man first decided that everything we see around us has to be the product of a powerful being or beings that look, act and think pretty much the same way we do.

Molecular Biology has is taking the lead in terms of validating evolution as a cogent theory. The attacks on Darwin's ideas by factions such as those who proport Intelligent Design are following along far behind the advances being made today.

It is amusing that religions touting a Creator God are excellent examples of Evolution in Action. The Creator God is the equivalent of the alpha male of a troop of primates. The idea of the Creator God speaks not to the present alpha male but to an idealized father founder of the tribe. The sense of history inherent in a Creator meshes with our sense of our own history. The concept of history, partially embodied in burial rites, points to the ideas of teleology and the status quo ante that underpin many religions. The idea of death as examplified in burial and a belief in a life after death are ideas that need to be examined as they define us as a species.

Religions posing an alpha male Creator Father have evolved through many generations of selective mating. Those who strongly believed in the tribe's faith were more likely to find suitable mates. Those who couldn't bring themselves to believe in a Creator God were often killed outright as heretics or were driven from the tribe. Many generations of mating based upon religious beliefs should give us a population the majority of which advocate a belief in God. Religion is Evolution in Action.

Your example isn't evolution. It's natural selection. You're talking about popualations being refined, not growing a new leg or being endowed through mutations to better survive a climate or environment.

The disbelievers will in the near future miss out on genetic enhancements/cloning/implants and thus be weeded out of the population as they become unable to compete. Problem will fix itself.

Probably not. A number of medical technologies we now consider part of the standard of care -- anesthesia, aseptic surgical technique, vaccination, x-rays, antibiotics, and blood transfusions all come to mind -- met with fierce challenges on religious grounds when they were first introduced. Over time, as the benefits

"All [cafepress.com] truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident."

Let me roger up, though, for the Bored Followers of Christ.
I rejoice in science framing the what of existence in increasing detail.
Still not doing much for the why of existence.
Nor are the various religions and philospies, Christianity among them. It remains subjective.
I'll just relax and watch the show.

"The researchers say the findings, published today in the journal Science, offer a counterargument to doubters of evolution who question..."

Can you believe it's 2006 and we still care about the near-high-school drop-outs who continue to question evolution?

I've found that most people who are ignorant of evolutionary processes lead sheltered lives. They are vaguely ignorant of where the beef on their table came from, they couldn't tell you how rainclouds form and they don't have a clue how much oil may b

Dr. Thornton said the experiment refutes the notion of "irreducible complexity" put forward by Michael J. Behe, a professor of biochemistry at Lehigh University.

We care because these yahoos get control of school boards and muck about with the science curricula in public schools. It's 2006, and it would be inexcusable not actively oppose them, because they have no intention to stop inflicting kids with "near-high-school dropout" level of science education.

I wonder if the people who answered yes to this really believe that:a) the dinosaurs never existedb) if they did, that it had no real effect on the ecology: things were still pretty much like they are now, just with dinos running around.

I mean, the era of the dinos are by the far most well-known geologic period other than our own. And you need only to have seen a few imaginative pics of this time to know that they lived in a radically different ecology: all different plants, all different creatures, very d

Partly because one of those near-high-school drop-outs is our president. And some others sit in Congress. And while I believe the federal government should have no say at all in local education the fact is they currently do. If they wanted to drop a school's federal funding because they teach evolution they can do it.

Can you believe it's 2006 and we still care about the near-high-school drop-outs who continue to question evolution?

For those of you who don't read science, I would like to add that the paper itself made no mention of ID at all. Of course, biologists are interested in evlotution of complex mechanisms for its own sake, not for the sake of convincing some young earth creationists.

However, Dr Christoph Adami, who wrote in Perspecives (basically, giving an opinion of the significance of a new finding and providing the non-specialist with a context of the paper) made the point of how fatal this finding is for the ID argument. Here we have parts that have exactly the "irreducable complexity" that ID proponents love to talk about, and now someone has managed to reconstruct their evolutionary history.

Can you believe it's 2006 and we still care about the near-high-school drop-outs who continue to question evolution?

As the article points out, near-high-school-dropouts aren't the only ones who have questions about evolution, and I'm not just talking about proponents of intelligent design.

But maybe it's not so much that we care about what those who "question evolution" think as that good science doesn't simply stick to whatever the prevalent dogma is. Maybe it's that good science continues to come up with a

Can you believe it's 2006 and we still care about the near-high-school drop-outs who continue to question evolution?

The problem is that evolution cannot be demonstrated making simple stuff into complex stuff before the eyes of observers and cameras. One has to except that truckloads of incremental and minor evidence can be extrapolated to the formation of complex life from simple life or mud. After being lied to by automechanics, lawyers, financial advisors, and marketers; people have formed a "show me" a

I'd say that the problem is that the evidence for evolution requires a lot of prior knowledge. You have to be reasonably well informed about: chemistry, genetics, bio-chem, statistics, geology, and the basic scientific method to put it all together. Most laypeople simply have neither the time nor the interest to devote to learning those things, much less looking at how all the evidence for evolution fits together.I'm not sure what the solution is, other than more education. Sadly, in the US at least, des

I'm a high school dropout and I'm both an athiest and I subscribe to evolution. I know a lot of college graduates who are very sharp and intelligent and yet don't accept evolution and believe in god.

Really, I think that the choice on this matter is often dicated by emotion, which overrides any intellectual consideration or presentation of facts. Some people are afraid of there not being a god, or don't like the feeling of not knowing the purpose of life, or just like sharing beliefs with their friends and families, or don't like to admit they've been wrong for the past forty years, etc.

And these people are important: they make up more than half of the voting population in my estimation so they have a profound effect on you and I. So don't dismiss them. And don't bother trying to convert them. But find a way to live with them. You may even find some of them make good friends.

I continue to question evolution, and I gradutated University with a Bachelor's of Science in Physics. However I haven't had a biology course since 10th grade, so I haven't had that much exposure to evolutionary ideas in a while. However, one of my main objections has been that nobody could explain in a detailed manner how a random mutation could every add functionality to an organism, so it is nice to see that such things can be explained. It makes evolution seem more plausible to me, although I haven't qu

Using genetic algorithms, if I randomly write bytes at 10M/sec to a hard disk long enough, I will eventually produce Windows Vista

You have no idea what you are talking about.

Genetic Algorithms are *NOT* about a million monkeys typing random garbage until you stumble upon the complete works of Shakespeare. You reveal a complete ignorance of what Genetic Algorithms are and how they work when you suggest such a thing.

I am a programmer and I have personally used Gentic Algorithms in the past. I have personally witnessed just how FAST they spontaneously generate information. How FAST they generate complex structured information. Sometimes they demonstrate slow steady improvements, and sometimes they generate huge leaps and bounds in solving problems.

The process by which evolution creates information is well understood, and has been the subject of many mathematical papers. The FACT that the evolution process can be harnessed to create information and solve problems has been extensively observed, documented, and USED in real industrial applications. In fact the Genetic Algorithms evolution process has been used to create new better more efficient jet engine designs, designs better and more efficent than any human expert has ever been able to design.

Genetic Algorithms are a powerful tool in the programmer's bag of tricks, and I highly reccommend that any and all programmers learn and explore them. Any programmer can easily witness ad understand for himself exactly how evolution is an information processessing system, and an information creation system. Can witess for themselves exactly how evolution can and does create information. Just pick up any book on Genetic Algorithms, or use Google to find any of the excellent websites on the subject.

And anyone who claims that evolution does not or cannot create information, well they are flat out Wrong and Ignorant. It's as silly as someone claiming that man can never build a heavier-than-air fling machine AFTER scientsists have understood and built and witnessed such machines working.

I've built it. I've witnessed it. And anyone who doubts it is absolutely invited to study Genetic Algorithms and understand it themselves and built it themselves and witness it themselves.

People who say evolution cannot create complex information and cannot produce the complexity of life we see today, those people warrant as much respect as someone claiming flying machines are impossible.

A sun-centered solar system explains the mechanism that divides the light from the darkness. It is absurd for anyone to suggest that a sun centered solar system in any way says or means that God does not exist. Nuclear fusion explains the mechanism that creates light for the earth. It is absurd for anyone to suggest that nuclear fusion in any way says or means that God does not exist. Optics explains the mechanism that creates rainbows. It is absurd for anyone to suggest that optics in any way says or means that God does not exist. And evolution explains the mechanism that creates the diversity of life on earth. It is absurd for anyone to suggest that evolution in any way says or means that God does not exist.

Anyone who suggests that evolution and God are in any sort of conflict is as bad as the crackpot fundamentalist idiots who had Galileo imprisoned for life when he said that the earth moves around the sun. The fact that so many people are replaying this exact same nonsense today is an absolute embarrassment.

"They won't even entertain any alternate theories to evolution anymore, even if it was made by a non-religious person."That's because, in science, you have to have evidence to back up what you say. If it were the case that scientists were just tossing away lots of convincing evidence against evolution and for another theory, you'd have a point. But instead, most of what they are being attacked with is hordes of poorly informed nonsense that's been dealt with a million times.

Carl Zimmer,who is of course, THE MAN! of parasite parables and paraphenalia, has posted a more in-depth
analysis [corante.com]
of this story at his weblog, The Loom [corante.com]
, going into the genetic/molecular mechanism. Additionally, Zimmer responds
to the creationist take [corante.com]
on the story (the usual move-the-goalpost panic of those advocating irreduceable complexity). Of larger concern, why does this incredibly fascinating discussion about scientific sleuthing and the potential and beauty of proteomics, get automatically sidelined into a discussion on "what does creationism say about this?" I don't blame Zimmer for responding; indeed, that's the duty of science writers as gifted as he. But it diminishes the power of the story itself to have to ask, imnsho.

It's worth noting that most mathematicians already think ideas like Irreducible Complexity and Complex Specified Information are a load of hooey, despite the appeals people like Dembski and Behe make to having made innovative breakthroughs in these areas:

One good blog on this subject I've found is Good Math, Bad Math, and some posts relevant to this topic are:

The study is a fascinating one. If you have a subscription to Science, I suggest reading the summary of the research by Cristoph Adami termed "Reducible Complexity." I'm sorry I don't know how to get that article to those without a subscription but I can give a lay-man's summary here. Although the original research did not specifically mention evolution vs. intelligent design, they essentially disproved the central tenet of ID, that of "irreducible complexity." IC states that some things are so complex, they look like a "lock and key" mechanism -- one could not have be made without the other "in mind" -- thus they must both have been designed. The research that is the focus of this article described two different hormones with two different receptors. Both look like lock and key systems. By tracing evolutionary lineages, the authors of the study showed how a series of mutations, as little as 2, occuring sequentially by random could have led to the two divergent lock and key systems from a single precursor. As an academic biologist, I really think this elegant study is one of the nicest pieces of evolution research to come out recently. It truly addresses a problem even Darwin admitted was a caveat (though Darwin also offered the solution, which was indeed confirmed here).

The solution is that the original precursor gained the ability to bind a new hormone by a single point mutation, and this did not disrupt the ability of it to bind its old hormone. The new receptor then diverged and through a well known process of gene duplication, begat multiple and independently evolving molecules. One retained the function of binding the old hormone, whereas another mutated further to lose the ability to bind the old hormone and could now only bind the new hormone. Viola -- two seemingly "designed" systems out of one precursor -- evolution at its finest, and IMHO, damning evidence against the basic principle of Intelligent Design.

On a personal note, it never fails to amaze me how much people deny the intelligence of humans to figure things out... the old "just because we can't explain it now, it must have be an unexplicable force, like God." I'm sure lightning and earthquakes seemed supernatural too. Evolution is no different -- it can be dissected and explained.

Yep. It's important to note that the functional abilities of proteins are often determined by just a few key sites (certain amnio acid sequences) which make the protein fold in a certain way. The rest of the protein is free to vary somewhat without making much of a difference. And sometimes, these sections can, through mutation, add a new function to the protein without taking away the old function: the new folding may not interfere with important part of the old shape.Of course, this "retain the old, tr

Another way to speak about reducible complexity is to use the analogy with compilers: originally, there was no compiler. Then somebody made a translator of the first programming language in assembler; then someone else wrote another compiler in this programming language etc. And now we have operating systems and compilers who seem to exist in "lock and key" status, but they were actually produced independently.

In the interests of good discussion, I'd like to answer any questions that those questioning or unfamiliar with evolution have about the basic idea. We always seem to get a lot of sniping and pile-ons, and cross debate on this subject, so I thought I'd at least offer a place to express doubts or ask somewhat more general theory questions. Most of what I'm best experienced with as regards to evolution is common descent, but I've been studying the subject for quite some time now both as an amatuer and as an

It is ridiculus and demeaning to all human scientific progress to suggest that articles published by researchers are to be used as a "counter argument" to ID.

Please compare: What is their argument and what is ths scientific argument ? Who and where are their researchers ? What "science" do these reseaerhers do ? Is it a coincidence that almost all of them are Fervent Christians ? Do these peope want REAL answers to questions in the Universe or have they decided their answers already ? Imagine what would happen if their "science" becomes mainstream in schools and Universities: Something similar to what would have happened if Nazi bigotry had become mainstream.

What I'm trying to say is, it is stupid, demeaning and a complete waste of time,for example, to present arguments of the level of Einsteins work to someones who's bigotry driven intelligence is barely comparable to a below average high schooler. (not to demean high schoolers).

The only way to tackle these lies is to hit the root of the Big Lie: Who, what and where is this I in ID that they speak of ? Showing them Science journal will come later.

After RTFA I have to say I'm impressed with this study. Science for far too long has neglected to roll its sleeves up and get to the nitty-gritty of how biochemical evolution might have occurred. Usually scientists show us a chart of, say, eyeballs, from the primitive light-sensitive patches of worms all the way to the more advanced eyeballs, like the humans. This is usually followed with some vigorous handwaving, capable of producing hurricane-like winds. "Behold! Evolution!" shouted with triumph, but

The gist of the paper seems to be that the belief that intertwined mechanisms had no purpose prior to their union is false. While we may not currently know what purpose the individual mechanisms originally served, it does not mean that they arose solely to work together. The belief that they arose to work together seems to be a sort of bias toward the present-day--an assumption that what there is now is somehow better than what there was in the past, and therefore the past must have been working solely to a

There are two reasons why we have a recent uprising of ID. One is that there are people whose religious beliefs are found in conflict with evolutionary science. The other is that people are simply ignorant of the science, in large part because of lousy science education and hard-to-read science literature.In response to the ID debate, scientists have been motivated to clean up their acts. First, they have targeted specific areas of research that the ID proponents have harped on. Secondly, they are worki

While I agree with some of your post but your statement "In response to the ID debate, scientists have been motivated to clean up their acts. First, they have targeted specific areas of research that the ID proponents have harped on." is way off. The principle job of a scientist is to do research and you directly state we're not doing our jobs. That's pretty offensive especially since research in molecular evolution started back in the 60's when ID was still called creationism. Thornton's research is ju

In response to the ID debate, scientists have been motivated to clean up their acts. First, they have targeted specific areas of research that the ID proponents have harped on. Secondly, they are working harder to improve science education.

Clean up their act? They're cleaning up other people's mess!Having throwbacks to pre-rational thinking dictate areas of research to target is a nuisance, not a boon. And they are working harder because they have to undo the harm that the ID conmen have caused, hard work t

Its established Paloentological fact that the Sabertooth Tiger has appeared, went extinct, and reappeared at least four times in prehistory. This is due to genetics. Every big cat and every domestic feline carries the genes that could become active again and thus bring about the reappearance of the Sabertooth.All one has to do is think of DNA as a complex computer program. It can correct itself if errors are found, and it can change itself to adapt. Its not hard to imagine that Evolution is a byproduct

I can't find any reference to this fact about the "reappearing Sabertooth" anywhere. Nor does it really make much sense that we could declare something extinct if there is fossil evidence that it existed after that period. Nor am I aware of any genes in domestic felines that can simply be turned on to produce a Sabertoth. So..... Cite?

The reason the NYT is giving this the "doubters of evolution" spin is that there's this guy, Michael Behe, who wrote a book around 1995 somewhere called "Darwin's Black Box". The central idea of that book was the allegation that evolutionary science treats the cell like a "black box" that nobody attempts to look inside or explain. Evolutionary science, said Behe, only concerns itself with larger structures, and only assumes the stuff inside the cell "just works". Because evolution can't explain, subcellular structures, evolution lacks a foundation, is built on nothing, and is wrong.

This is, of course, silly if you're actually familiar with the science, because to whatever extent scienists ever treated the cell like a "black box", it was because we didn't know how to look inside yet. Viewing machinery the size of a molecule is really hard. Scientists could analyze things, but have only relatively recently gained the ability to view the full picture of things, much as they might have wanted to.

Once the technology for understanding the molecular structures that make up cells really started to take off (say, at the beginning of the 80s-ish), a revolution of sorts started in microbiology and genetics. And as this happened, Behe managed to exploit a neat trick of timing; he wrote his book just as a lot of fascinating questions were appearing through this revolution in microbiology, but before (since the questions had only just been asked) we really knew what the answers were. Behe was able to craft the illusion, since we didn't know the answers to some of those questions yet, that the questions didn't have answers or would never be answered and thus evolution was flawed-- not mentioning that work was underway or even partially completed to find answers to all of these questions. In the time since Behe wrote his book, cell microbiology has progressed by leaps and bounds, but the book itself is able to do a neat little job of making it seem like the cell really is just an inexplicable black box, because he wrote it just as science totally finished picking the lock.

Which brings us to this story: The one scientific "big idea" in Darwin's Black Box was what Behe calls "Irreducible Complexity", and the publication of Darwin's Black Box was the main way this idea was popularized. The idea behind irreducible complexity is that there exist structures that contain one or more parts, and that if you remove one of the parts, the entire thing stops working. But one would expect that evolutionary mutation can only change "one thing" at a time; the idea that a single new allele that could simultaneously create two separable and interlocking structures seems wholly unbelievable. So how did irreducibly complex structures evolve?

This is an extremely reasonable question, and one evolutionary science is obligated to answer. The problem is that Behe, and the rest of the ID crowd:

Instead of asking the question, "how did irreducibly complex structures evolve?", skipped the question and immediately jumped to the conclusion "it is impossible for irreducibly complex structures to evolve".

Even after answers to the question saying "this is an explanation of how irreducibly complex structures can evolve" were provided again, and again, and again, kept doggedly insisting "it is impossible for irreducibly complex structures to evolve".

The answer to how irreducibly complex structures could evolve is pretty simple: all that would have to happen is for a structure to change its purpose over time. That is to say, it doesn't matter that irreducibly complex structures can only evolve one part at a time, because it is simple to imagine each of the small structures in an irreducibly complex system independently evolving for some other purpose than the big IC system performs, then being adapted into a bigger IC system with rube goldberg style ingenuity, then gradually losing the ability to function for their original purpose indepen

That should be: Can God create a stone so heavy he can't lift it, if he can, he's not all powerful because he can't lift the stone, if he can't he's not all powerful because he can't create the stone in the first place.

indeed, some time ago i saw a movie that tried to "proof" the qoran as a "true" book of god. I found it quite of funny to see that they sad things along this line:1. well, we see the stars moving away from each other so the universe must be expanding.2. so if they are moving away from each other there must have been a beginning point, a "big bang" place3. that is where allah created the universe.

the previous pope held a simulair belief.

while I neither believe in Islam nor in Christianity i do believe that r

First: Science does not deal with truths, only with models.Second: Science cannot be applied everywhere. There are questions that cannot be answered by science, because no answer fulfills the requirements. (Like, "what is outside of the universe", or "why are we here".) There comes a point where the only thing you can do is - believe. In something. Some believe that there are no higher entities (science cannot disprove them, but because of this they are filtered out by Occam's Razor, just like all non-dispr

For many the term science refers to the organized body of knowledge concerning the physical world, both animate and inanimate, but a proper definition would also have to include the attitudes and methods through which this body of knowledge is formed; thus, a science is both a particular kind of activity and also the results of that activity.

When we talk about evil, people usually attribute it to Satan. However, Satan was first created to be the most beautiful being of all things, anointed as a guardian cherub and adorned with precious stones in the garden of Eden (Ezekiel 28:11-19). But he chose to betray God.If you look up Ezekiel online, note that subject in Ezekiel's discourse is King of Tyre, but Tyre is used to allude to Satan.

God did not create evil. His most beautiful creation turned evil on him. God knew this would happen and already f

My understanding is too shallow to answer this question, but I believe that God is doing this for a globally optimal solution.

I credit you with admitting that you don't understand it either. But that's the problem, I think. I'm not saying I can understand everything, and I don't think that life is a net loss (i.e. I believe there is more good than evil). But it seems quite understandable that any all-knowing, all-powerful, all-good God could allow the evil that has happened to have happened. And saying

This is an excellent question that causes a great deal of controversy. Since every possible outcome, event and possibility is happening and will happen, then all good and all evil balances out in the superverse. After the reality of multiple worlds sank into our collective thought, the one basic change to all religious dogma is the concept that good and evil does not exist as an organized force in our lives nor can it be used as a useful way to judge what God may think of a situation. Good and evil are per

So you managed to pass philosophy 101 and think that because you can take the most pithy argument about the problem of evil and 'prove' god does not exist. Alvin Plantinga, a standing professor at Notre Dame, dealt extensively with the problem of evil and has several books on the topic. Many philosophers, even those who categorize themselves as secular, generally agree that Plantinga's Free Will Defense is a logical and mostly complete answer to the questions the problem of evil poses. Johnathan Kvanvig,

You are a moron. Before I'm modded down as flamebait I shall justify that statement.

When science thinks they understand something, credit should be made to God.

Science is not a person. Science is not plural.

But God has been here FOREVER!!

Just saying this in capital letters doesn't make it so.

He has been proven to be true.

Propositions or sentences are proven to be true. 'True' isn't an adjective that can be applied to characters from mythology. Maybe you mean "He has been proven to exist." But your inability to construct meaningful sentences is already losing you credibility.

Unlike any other religion or science...

What is the subject of this sentence? Are you saying that Christianity, the religion, sent Jesus. Or that God did? Do you have any idea what you are saying and how to construct a sentence.

That's okay, we can look at this matter in a more light hearted way.Imagine a scientist looks at an ancient CVS repository of the Linux kernel and notices that the source code evolves and branches. He is able to compute the diffs between each source code revision and to recall an early snapshot of the Linux kernel. He concludes that the code must have evolved on its own.

Moreover, he claims this justifies that Linux kernels must have evolved from a monocellular organism, which kind of makes sense because Lin

The existence of evolution is not inconsistent with the existence of god. Most scientists agree on that point.

The most common people to claim otherwise seem to be the more rabid IDers and creationists. Go figure.

And for the most rabid athiests, I would point out that lack of proof is not proof of lack -- eg: Just because you'll never find the body doesn't mean I never killed mikie (don't tell the cops). Similarly: the fact that a 'missing link' is currently missing doesn't mean that it will never be found.

When it comes to evolution, I don't think there is really a "missing link" anymore.The theory is fairly well fleshed out. Scientists and archeologists know what they're looking for, where they're looking for it and when (in the past) it should be found. The only thing a "missing link" can do now, is to reinforce & reconfirm the existing theory.

What will be much more interesting from a science perspective, are animals or chemical processes that don't fit in with the existing body of knowledge. Those are

Indeed. Most scientists roll their eyes at the use of "missing link" because it obviously misleads far more than it informs. The basic idea is that we have a family tree of life. There are millions upon millions of branches (species), and billions upon billions of twigs (individual creatures) alive over time, but only a very very tiny proportion are still alive today. That means that there is a far far vaster space of animals that died that are NOT the ancestors of any living creature than there are.

Hence, since fossilization is basically a rare and random crapshoot, the chances of finding THE common ancestor are always unlikely, and we can't even reliably tell if we had. But, fortunately, it's also irrelevant. That's because we can learn more than enough simply by finding a fossil that's past a particular branching point about the creatures that led to those we see today. We are trying to learn the general, overall shape of the tree, and since features all tend to be unique to any given lineage, we can still always tell everything we need about the prior branchings from the random sampling of fossils we have.

Currently we have so many that all the basic connections are pretty clear. And when you add in genetic studies that confirm these relations, the conclusion becomes about as rock solid as can possibly be. Creationists often try to confuse the debate over how particular twigs branch with a debate over whether there even is a tree of life pattern and branching at all.

My point is that, even if one accepts that a missing link 'exists', that only proves that it hasn't been found, and not that it won't. It's the finding of other (previously) missing links which 'prove' that whatever links may currently be deemed as 'missing' are more likely to be found than not (with appropriate resources).

That something has not been found doesn't prove anything by itself. For the lack of proof to be considered proof of lack, you would also have to prove that you've created (usually co

They are claiming that God couldn't have made those enzymes, or the manner in which they function.

The letter string "God" did not occur anywhere within the article. I believe that you have misinterpreted the claims made in the article, or you have mistaken read a different article than the one referenced. Your conclusion cannot be drawn from the actual article.

I predict we can make millions selling the smaller ones to Creationist families. After all, don't they want to be closer to the original man?

I can see the ad campaign now: Get your child a pet dinosaur so they can ride them just like man did before the flood! Now you too can have a beast of the earth, just as God gave to Adam! (Discounts given to Church groups buying more than 3 pet dinos.)

I don't know that we have as of yet been able so show a living cell bootstrap from basic inert materials (I'm using non-living as the definition of inert in this context. There may be a better word, but I didn't think "dead" would be appropriate, as it has an implication of "once was living".)

However, it has been shown that many organic materials can be created in an environment similar to primordial earth. It has also been shown that many of these materials do tend to self-organize in a way that would be compatible with a cell possibly forming given enough organic material and time.

Cell wall: phospholipids, mostly being hydrophobic with one or two ends being hydrophilic tend to organize in sheets or water filled bubbles, and so could naturally form a cell wall. Amino acids do self aggragate to some extent, and a random aggregation could form a useful protein, ditto for RNA (which I believe preceded DNA evolutionarilly for a number of reasons.)

There is only one protein that would have to aggregate naturally before life as we know it could arise... ribosomes (or some suitable analog.) From there RNA could be transcribed into protein. At first most of the protein would pretty much be useless globs, untill a protein arises that can create copies of RNA. This protein could either aggregate naturally or be encoded by random chance into a strand or RNA. From there Darwinian evolution kicks in and as more beneficial RNA sequences come about that improve the transcription process and copying mechanism as well as the defense mechanisms, cellular life would not be too wild of an outcome. The progression of life would seem to be fairly slow at first, but the copying mechanism in RNA would probably be so imperfect that new variations arise very frequently, but most of those variations would likely be detrimental. Eventually better copying mechanisms arise, and eventually use of a more stable genetic material (DNA) make life blossom, expanding at a decent pace. Once some organism figured out a way to systematically capture and store energy from sunlight (or any energy source, really... thermal vents, gradiants across a thermo/chemocline etc) and a way to release that energy, then evolution can start proceeding at an exponential rate.

So, if it can be proven that a ribosome or some other RNA-Protein copying method could eventually arise from a random mix of amino acids it would greatly support the possibility of some method of abiogenesis. It does not have to be likely that this ribosome would arise in a human time scale... it could take millions or billions of years. It just has to happen eventually.

Complex hemes, carbohydrates and many other materials that are necessary for life at a complexity of ours would not be necessary to bootstrap the system from inert materials. Just some strands of RNA and something like a ribosome. Once you have those, something as complex as an RNA transcriptase could eventually arise from random permutations of RNA strands. And once you have RNA that has RNA -> RNA transcriptase encoded somewhere inside of itself and has some ribosome analogue working on it, then you have the bare bones beginning of organic life.

You had me worried for a little bit, so I did some looking around. Modern theories state that it wasn't even RNA that was the original genetic carrier, but self replicating proteins. Turns out it would have statistically taken somewhere around the order of one year [talkorigins.org] for the creation of a self replicating protein to arise on the primordial earth. That gives plenty of time for that self replicating protein to have a couple of chances at being in the right place at the right time in the right conditions to b

Those terms are not "owned" by ID proponents. The language is very common in biology. We often say the "cell" reuses this and modifies that. Or that a certain protein can modify another protein by attaching a tag to it. Whole classes of enzymes may be termed "modifying enzymes". The point is that these are models for what is essentially a chemistry reaction (which itself is essential a problem in physics). One should not have to describe every atomic configuration every time one wants to discuss an en

Where did you come up with comparison of the Uncertainty principle to ID. IIRC Heisenberg's prinicple said that observing something changes it's behavior, thus making it uncertain. I can think of many areas where this is true, but ID or evolution already happened. We can neither observe it, or change it. We are all already here. All that can be done now is attempt to prove in a laboratory that evolution is possible, which still doesn't prove that it happened.